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- PDB-5c51: Probing the Structural and Molecular Basis of Nucleotide Selectiv... -

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Basic information

Entry
Database: PDB / ID: 5c51
TitleProbing the Structural and Molecular Basis of Nucleotide Selectivity by Human Mitochondrial DNA Polymerase gamma
Components
  • (DNA polymerase subunit gamma- ...) x 2
  • DNA
  • DNA (5'-D(*(AD)P*AP*AP*AP*CP*GP*AP*GP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*GP*TP*AP*C)-3')
Keywordstransferase/dna / Nucleoside reverse transcriptase inhibitors (NRTIs) / HIV RT / human mitochondrial DNA polymerase / mitochondrial toxicity / drug efficacy and toxicity / transferase-dna complex
Function / homology
Function and homology information


gamma DNA polymerase complex / mitochondrial chromosome / mitochondrial DNA replication / Strand-asynchronous mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / DNA polymerase processivity factor activity ...gamma DNA polymerase complex / mitochondrial chromosome / mitochondrial DNA replication / Strand-asynchronous mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / DNA polymerase processivity factor activity / mitochondrial nucleoid / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / base-excision repair, gap-filling / DNA polymerase binding / 3'-5' exonuclease activity / Transcriptional activation of mitochondrial biogenesis / base-excision repair / DNA-templated DNA replication / protease binding / double-stranded DNA binding / in utero embryonic development / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrial matrix / intracellular membrane-bounded organelle / chromatin binding / protein-containing complex / mitochondrion / DNA binding / identical protein binding / cytoplasm
Similarity search - Function
DNA-directed DNA-polymerase, family A, mitochondria / DNA mitochondrial polymerase, exonuclease domain / POLG2, C-terminal / : / DNA mitochondrial polymerase exonuclease domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding domain / DNA polymerase family A / Anticodon-binding / Anticodon binding domain ...DNA-directed DNA-polymerase, family A, mitochondria / DNA mitochondrial polymerase, exonuclease domain / POLG2, C-terminal / : / DNA mitochondrial polymerase exonuclease domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding domain / DNA polymerase family A / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1RY / DNA / DNA (> 10) / DNA polymerase subunit gamma-1 / DNA polymerase subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Virus Chimp162
DNA launch vector pDE-GFP2 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.426 Å
AuthorsSohl, C.D. / Szymanski, M.R. / Mislak, A.C. / Shumate, C.K. / Amiralaei, S. / Schinazi, R.F. / Anderson, K.S. / Whitney, Y.Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma.
Authors: Sohl, C.D. / Szymanski, M.R. / Mislak, A.C. / Shumate, C.K. / Amiralaei, S. / Schinazi, R.F. / Anderson, K.S. / Yin, Y.W.
History
DepositionJun 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Other
Revision 1.2Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / ndb_struct_na_base_pair / pdbx_entry_details / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.details / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase subunit gamma-1
B: DNA polymerase subunit gamma-2, mitochondrial
C: DNA polymerase subunit gamma-2, mitochondrial
P: DNA (5'-D(*(AD)P*AP*AP*AP*CP*GP*AP*GP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*GP*TP*AP*C)-3')
T: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,0048
Polymers260,4685
Non-polymers5363
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16790 Å2
ΔGint-77 kcal/mol
Surface area84890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.049, 215.049, 161.692
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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DNA polymerase subunit gamma- ... , 2 types, 3 molecules ABC

#1: Protein DNA polymerase subunit gamma-1 / Mitochondrial DNA polymerase catalytic subunit / PolG-alpha


Mass: 136033.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLG, MDP1, POLG1, POLGA / Cell line (production host): sf9
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P54098, DNA-directed DNA polymerase
#2: Protein DNA polymerase subunit gamma-2, mitochondrial / DNA polymerase gamma accessory 55 kDa subunit / p55 / Mitochondrial DNA polymerase accessory ...DNA polymerase gamma accessory 55 kDa subunit / p55 / Mitochondrial DNA polymerase accessory subunit / MtPolB / PolG-beta


Mass: 54991.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLG2, MTPOLB
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9UHN1, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules PT

#3: DNA chain DNA (5'-D(*(AD)P*AP*AP*AP*CP*GP*AP*GP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*GP*TP*AP*C)-3')


Mass: 6779.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: AAAACGAGGGCCAGTGCCGTAC / Source: (synth.) Virus Chimp162
#4: DNA chain DNA


Mass: 7672.917 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA launch vector pDE-GFP2 (others)

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Non-polymers , 2 types, 3 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-1RY / [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 487.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13FN3O12P3S

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.62 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG4000, KCl, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.42→50 Å / Num. obs: 50770 / % possible obs: 95 % / Redundancy: 8 % / Net I/σ(I): 2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 3.426→47.017 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 43.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3449 1990 3.94 %
Rwork0.3149 --
obs0.3161 50478 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.426→47.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13634 957 30 0 14621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315078
X-RAY DIFFRACTIONf_angle_d0.75520629
X-RAY DIFFRACTIONf_dihedral_angle_d14.8695658
X-RAY DIFFRACTIONf_chiral_restr0.0282222
X-RAY DIFFRACTIONf_plane_restr0.0042473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.426-3.51170.47291190.47662879X-RAY DIFFRACTION83
3.5117-3.60660.50751420.43413450X-RAY DIFFRACTION100
3.6066-3.71270.46181440.42793490X-RAY DIFFRACTION100
3.7127-3.83250.48411410.43953452X-RAY DIFFRACTION100
3.8325-3.96940.44861430.3863469X-RAY DIFFRACTION99
3.9694-4.12820.39721420.37233458X-RAY DIFFRACTION100
4.1282-4.3160.39131410.36213478X-RAY DIFFRACTION99
4.316-4.54340.37251430.35183472X-RAY DIFFRACTION99
4.5434-4.82770.38121400.33483482X-RAY DIFFRACTION99
4.8277-5.20010.33581440.32583495X-RAY DIFFRACTION99
5.2001-5.72250.37171450.32573536X-RAY DIFFRACTION100
5.7225-6.54870.34181450.33533549X-RAY DIFFRACTION100
6.5487-8.24340.31421480.30673606X-RAY DIFFRACTION100
8.2434-47.02170.28151530.23653672X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.102-0.08390.18310.8926-0.79623.09740.0653-0.1935-0.1652-0.1288-0.1695-0.35760.40470.3390.01561.33610.007-0.02281.10070.13831.599363.9798-35.592624.5051
2-1.2034-1.0778-1.61453.62030.96781.47070.25520.0378-0.4105-0.3677-0.17280.39490.00330.01910.03731.0179-0.1565-0.11551.19070.19341.609245.9603-1.295927.7705
31.8007-0.5631.17610.865-0.1068-0.53650.28860.54330.1835-0.4874-0.09750.18720.25670.00690.01431.607-0.0958-0.04181.24860.18690.97953.3172-28.07650.8368
48.494-0.6086-0.02824.96110.12220.3817-0.5115-0.91360.65620.19340.4807-0.8537-0.29410.6229-0.1621.45140.07920.2581.08960.13340.45868.469228.221730.0144
54.37541.0847-1.23382.76570.67823.12010.4110.47-0.8822-0.6642-0.3419-0.09620.26660.04210.12681.34030.03080.19091.19680.09371.108468.217321.100319.8683
67.26490.00294.47075.9729-3.00314.2524-0.7776-0.02330.90381.11472.2152-2.8945-0.96071.99990.48051.45520.64020.57962.120.16062.154392.664420.768420.4487
72.54680.4143-4.04512.2710.16286.54730.0184-0.2195-0.2686-0.1726-0.2356-1.2804-0.2590.34860.29060.98430.12520.08281.043-0.01551.182871.305819.527223.5905
84.64143.84540.80776.1554-2.81633.8229-0.07621.64761.47230.0622-0.07010.117-0.5827-1.770.3421.40970.16430.331.44760.17731.561641.993123.894939.2003
93.25022.9380.346.8202-1.18698.6627-0.1080.1333-0.07481.0243-0.15110.7541-1.022-0.90490.27691.39370.07360.21631.29330.2171.544644.706821.420849.1116
104.1231-3.77322.57025.0159-3.69534.8250.83910.1569-0.1993-0.4285-1.36161.11760.1955-0.10330.03881.326-0.2408-0.16691.1883-0.0841.730377.827933.477842.118
116.9109-3.22512.24679.20892.02812.7528-0.58060.18151.31550.51580.2005-0.77-0.57740.19530.31661.7048-0.0227-0.13521.05750.2381.303668.094744.31849.9472
123.2425-1.4022-0.81394.32472.08782.56470.0840.16320.4197-0.36140.226-0.6426-0.24810.3787-0.58451.42370.0056-0.25371.24170.28591.163781.94677.437550.1192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 78 through 417 )
2X-RAY DIFFRACTION2chain 'A' and (resid 418 through 894 )
3X-RAY DIFFRACTION3chain 'A' and (resid 895 through 1228 )
4X-RAY DIFFRACTION4chain 'B' and (resid 68 through 205 )
5X-RAY DIFFRACTION5chain 'B' and (resid 206 through 306 )
6X-RAY DIFFRACTION6chain 'B' and (resid 307 through 325 )
7X-RAY DIFFRACTION7chain 'B' and (resid 326 through 352 )
8X-RAY DIFFRACTION8chain 'B' and (resid 353 through 395 )
9X-RAY DIFFRACTION9chain 'B' and (resid 396 through 485 )
10X-RAY DIFFRACTION10chain 'C' and (resid 67 through 186 )
11X-RAY DIFFRACTION11chain 'C' and (resid 187 through 353 )
12X-RAY DIFFRACTION12chain 'C' and (resid 354 through 485 )

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